Estimation of Execution Parameters for k-Wave Simulations

Estimation of execution parameters takes centre stage in automatic offloading of complex biomedical workflows to cloud and high performance facilities. Since ordinary users have no or very limited knowledge of the performance characteristics of particular tasks in the workflow, the scheduling system has to have the capabilities to select appropriate amount of compute resources, e.g., compute nodes, GPUs, or processor cores and estimate the execution time and cost. The presented approach considers a fixed set of executables that can be used to create custom workflows, and collects performance data of successfully computed tasks. Since the workflows may differ in the structure and size of the input data, the execution parameters can only be obtained by searching the performance database and interpolating between similar tasks. This paper shows it is possible to predict the execution time and cost with a high confidence. If the task parameters are found in the performance database, the mean interpolation error stays below 2.29%. If only similar tasks are found, the mean interpolation error may grow up to 15%. Nevertheless, this is still an acceptable error since the cluster performance may vary on order of percent as well

Magnetic-field-induced phase transitions in the quasi-one-dimensional organic conductor HMTSF–TCNQ

Motivated by an interest to see if the field-induced (FI) phase in the charge-density wave (CDW) system is similar to the field-induced-SDW (FISDW) in (TMTSF)₂X, (TMTSF: tetramethyltetraselenafulvalene), we examined the magnetic-field-induced phases in a quasi-one-dimensional (Q1D) organic conductor HMTSF–TCNQ (hexamethylene-tetraselenafulvalene-tetracyanoquinodimethane) under a pressure of 1.1 GPa, where the CDW occurring at 30 K is suppressed. The work was carried out by measurements of angular-dependent magnetoresistance oscillations and exploratory work on the Hall effect. It turned out that the FI-phase, most likely a FICDW for B > 0.1 T, accompany a quantum Hall effect, and the FI-phase transitions are controlled by the field component along the least conducting axis. Above 10 T, the lowest Landau level of the small 2D Fermi pocket (due to incomplete nesting of Fermi surface) exceeds the Fermi level, reaching the quantum limit. Although there are many differences between the CDW (HMTSF–TCNQ) and SDW ((TMTSF)₂X) systems, a similar scenario for field-induced phases seems to hold

Pleural effusion in long-term hemodialysis patients

As a consequence of the expanded use of long-term hemodialysis and extended life spans, complications of chronic renal failure are encountered with an increased frequency among uremic patients. Such patients may develop many thoracic and extrathoracic problems - most frequently uremic pleuritis and pericarditis, uremic pneumonia, infection, and metastatic pulmonary calcification. We retrospectively analyzed the medical records of 257 patients who had received long-term hemodialysis between 1990 and 2006 to better understand the incidence, causes, and clinical features of pleural effusions in this population. The incidence of pleural effusion in hospitalized patients receiving long-term hemodialysis was 20.2% (n = 52; mean age, 55.83 +/- 16.56 years; male-to-female ratio, approximately 3:2). Pleural effusion resulted from hypervolemia in 61.5% and was bilateral in 68.8% of patients. Unilateral effusion was present in 25 of 52 (48%) patients. The most frequent causes of unilateral effusion were hypervolemia (n = 9) and parapneumonic effusion (n = 5). Thoracenteses were performed in 14 of the 52 patients in the study group. Of thoracenteses performed, 64.3% of the patients had transudative pleural effusion and 35.7% had exudative effusion. Transudative pleural effusion resulted from hypervolemia in 66.7% and heart failure in 22.2%. Of the patients with transudative effusion, 85.7% were bilateral. The most frequent cause of exudative pleural effusion was uremic pleuritis, which occurred in 40% of the patients. The most common symptom was dyspnea, which occurred in 53.8% of patients. In conclusion, pleural effusions are common in patients receiving chronic hemodialysis. Thoracentesis may be performed in patients with unilateral pleural effusion. Since hypervolemia was the most common cause of pleural effusion, this complication should not be considered an obstacle in renal transplant recipients

Recent developments in studies on biological functions of vitamin A in normal and transformed tissues

A biochemical pathway of phosphorylation and glycosylation of vitamin A has recently been found in hepatic, intestinal and epidermal tissues. More recent work suggests that mannosylretinylphosphate functions as a donor of mannose to membrane glycoconjugates. These reactions might ultimately explain the effects of vitamin A deficiency and some of the effects of excess vitamin A on biological systems. Studies of the effect of retinoids on cellular in vitro systems showed an increase in the adhesive properties of spontaneously-transformed mouse fibroblasts in culture (Balb/c 3T12-3 cells). These cells are usually detached from the culture gish surface ig an EDTA adhesion assay. After culturing in presence of 3.3 x 10- to 3.3 x 10- M retinol or retinoic acid the cells are no longer lifted from the plate and their morphology and adhesion resemble those of normal fibroblasts. This phenomenon of increased adhesion is observed as early as two days after exposure to the retinoid and it is readily reversible upon culturing in medium without exogenous retinoid. A variety of retinoids was tested in the adhesion assay. The most active compounds were retinol, retinylphosphate, retinoic acid, 5,6-epoxyretinoic acid and the TMMP and DACP derivatives of retinoic acido All these compounds possess biological activity in other systems. Anhydroretinol, perhydromonoeneretinol, the" phenyl derivative of retinoic acid, which do not have biological activity in other systems, did not increase adhesion of 3T12 cells. Other polyprenoid compounds without vitamin A activity were also test ed in this assay. Dolichol, dolichylphosphate juvenile hormone, abscisic aCid, s-ionone, dibutyryl cyclic adenosine monophosphate and sodium butyrate did not induce adhesion. The mechanism by which retinol and retinoic acid increase the adhesive properties of 3T12 cells was investigated. Cyclic adenosine monophosphate and guanosine monophosphate levels were not significantly altered by retino~d treatment at least at 6, 24, 48 and 72 hours after treatment with 3.3 x 10- M retinoic acid, when most30f the cells remain attached. Retinoic acid stimulated the inc~rporation of (2- H) mannose into glycoproteins of 3T12 cells. (11, 12 H and carboxyl-14C)Retinoic acid was incorporated into a compound (Metabolite I) which had chromatographic properties of a glycosylretinylphosphate. The synthesis of this compound was time-dependent and was not carri ed out by formalin -fixed 3T12 cells. Mild alkaline conditiQns which release anhydroretinol from retinylphosphate, also cleaved Metabolite I to yield a product with the polarity of a hydrocarbon, but slightly more polar than anhydroretinol. It is suggested that retinoic atid can be reduced to an alcohol, probably after metabolic modification. It is further suggested that such "reti nol-l i ke" compound woul d fo" ow the same route of phosphoryl at ion and glycosylation as shown for retinol in other systems. Microsomes from 3T12 cells were active as the intact cells in synthesizing mannosylretinylphosphate and dolichyl mannosylphosphate. Exogenous retinylphosphate specifically stimulated the synthesis of mannosylretinylphosphate. Thus it appears that vitamin A is involved in glycosyl transfer reactions in the 3T12 system, as well as in normal membranes. It remains to be established whether the observed increased adhesion is the result of such involvement. A novel reaction for retinol was found in 3T12 cells. Up to 55% of exogenously supplied retinol was converted to the hydrocarbon anhydroretinol in 48 hours. The same reaction was also carried out by microsomes from 3T12 cells, which converted 7% of retinol toanhydroretinol in 30 minutes at 370C. This reaction may well represent a detoxification mechanism for the transformed cell